Ignore Hibernate @Where annotation
After lots of research it appears that this is simply impossible. I'd strongly suggest avoiding @Where, as it is hard to predict beforehand if you'll ever need those associations or not.
I just had the same question. I solved the problem like this:
@Query(value="SELECT * FROM EntityA", nativeQuery=true)
public ignoreWhereMethod(){}
The SQL in the @Query annotation must point the table's name and the fields' names (not entity's name).